ROCHESTER — The City Council on Tuesday approved raises for Police Chief Mike Allen and Police Deputy Chief Scott Dumas, but voted against merit-based salary raises for police command staff.

Before Allen became police chief in June, he signed a negotiated employment agreement with the Police Commission, stating that his $95,000 base salary would increase by $2,000 in December, and by another $2,000 in June.

According to Mayor T.J. Jean, the City Council is the only entity that can appropriate funds; therefore, a vote by the council took place Tuesday on whether to allow the salary adjustment listed in the contract.

As Allen was promoted to chief of police, Dumas, who was a police captain at the time, was promoted to deputy chief, and in April the Police Commission voted to have Dumas’s salary increase by $2,000 after six months of holding that position.

At the end of May, both Allen and Dumas also received raises due to their promotions — Allen’s salary went up by $4,990, and Dumas’s salary, which is now $83,000, went up by about $3,585.

While there was previously a question on whether Allen’s employment agreement would be honored by the city, when it came to salary adjustments listed in the contract, the council on Tuesday voted 11-1 to fund salary adjustments, totaling $6,000, for both Allen and Dumas.

Michele Small, administrator of the inspection division with the Labor Department, said before Tuesday’s meeting that Allen has made a claim with the Labor Department. She would not release further information without a Right-to-Know request.

Allen would not comment Tuesday about the claim with the Labor Department.

“It’s a personnel matter at this point, between me and the city,” he said before Tuesday’s City Council meeting.

After the meeting, Allen said, “They’re honoring my contract in totality,” and chose not to comment on whether the claim to the Labor Department will be dropped.

“I’m pleased that my contract has been resolved,” said Allen.

In another vote, the City Council chose not to increase the amount of funds available for salary increases for non-union police command staff.

While preparing the budget for the current fiscal year last spring, the council appropriated enough money in the merit pool to pay for an average of 2.5 percent salary raises to about a dozen non-union employees in the city, the majority of whom are police command staff.

In the Police Department budget, the council appropriated $12,027 for these salary adjustments — enough to give 2.5-percent increases to each non-union police staff member, said Jean.

Because the salary increases are merit-based, it was up to the Police Commission to decide how to distribute the pool of money based on performance evaluations.

While the council had appropriated $12,027 toward non-union police staff raises, the Police Commission proposed to spend $18,303 on the raises instead — enough to pay for salary increases averaging 3.25 percent.

While the City Charter states it is the Police Commission that is responsible for setting police wages, Councilor David Walker said only the council can appropriate money. He said that merit-based salary increases must be confined by how much is appropriated in the city’s merit pool.

“You can’t give money above the merit pool,” said Walker.

But Police Commission Chairman James McManus said the commission has followed the procedures highlighted in the merit plan, which outlines how merit-based salary increases should be administered and what the pay range is for various non-union positions in the city.

Allen said he has not seen anything in the merit plan that states the level of salary adjustments must be constrained by how much is appropriated in the merit pool.

Before voting on the issue, Councilor Sandra Keans suggested the merit plan be amended to remove any ambiguity about how performance-based raises should be administered.

The council on Tuesday voted 11-1 against increasing the amount of money available for salary adjustments. Councilor Alan Reed-Erickson voted in favor of allowing the higher salary increases.

Before the vote, Jean said sticking to 2.5 percent increases on average would be equitable — he said that’s the level of raises that employees working at the City Hall have seen this year. He also said that police command staff for whom the higher salary increases are proposed are some of the highest paid employees of the city.